Strain identifier

BacDive ID: 1480

Type strain: Yes

Species: Virgibacillus proomii

Strain Designation: BO413, F 2737/77, F2737/77, B0413

Strain history: CIP <- 1999, N.A. Logan, Glasgow Caledonian Univ., UK: strain B0413 <- PHLS, Colindale, London, UK: strain F2737/77

NCBI tax ID(s): 84407 (species)

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General

@ref: 4888

BacDive-ID: 1480

DSM-Number: 13055

keywords: 16S sequence, Bacteria, facultative anaerobe, spore-forming, Gram-positive, motile, rod-shaped, colony-forming

description: Virgibacillus proomii BO413 is a facultative anaerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from water supply.

NCBI tax id

  • NCBI tax id: 84407
  • Matching level: species

strain history

@refhistory
4888<- LMG
121962CIP <- 1999, N.A. Logan, Glasgow Caledonian Univ., UK: strain B0413 <- PHLS, Colindale, London, UK: strain F2737/77

doi: 10.13145/bacdive1480.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Virgibacillus
  • species: Virgibacillus proomii
  • full scientific name: Virgibacillus proomii Heyndrickx et al. 1999

@ref: 4888

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Virgibacillus

species: Virgibacillus proomii

full scientific name: Virgibacillus proomii Heyndrickx et al. 1999

strain designation: BO413, F 2737/77, F2737/77, B0413

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
23061positive2.0-8.0 µm0.5-0.7 µmrod-shapedyes
121962positiverod-shapedyes

colony morphology

@refcolony sizecolony colorcolony shapeincubation periodmedium usedhemolysis ability
230611.0-4.0 mmcreamy-greycircular2 daystrypticase soy agar
1219621

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4888NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: NaCl 30.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
23061trypticase soy agaryes
39486MEDIUM 316 - for Bacillus subtilis subsp. spizizeniiyesDistilled water make up to (1000.000 ml);Manganese II sulphate monohydrate(5.000 mg);Agar (15.000 g);Peptone (5.000 g);Beef extract (3.000 g)
121962CIP Medium 316yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=316

culture temp

@refgrowthtypetemperature
4888positivegrowth30
23061positivegrowth15.0-50.0
23061positiveoptimum37.0
39486positivegrowth30
121962positivegrowth22-45
121962nogrowth10
121962nogrowth55

culture pH

  • @ref: 121962
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23061facultative anaerobe
121962obligate aerobe

spore formation

@refspore descriptiontype of sporespore formation
23061spherical to ellipsoidal,terminal or sometimes subterminal, in swollen sporangiaendosporeyes
121962yes

halophily

@refsaltgrowthtested relationconcentration
121962NaClpositivegrowth2-4 %
121962NaClnogrowth0 %
121962NaClnogrowth6 %
121962NaClnogrowth8 %
121962NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23061168082-dehydro-D-gluconate-builds acid from
23061174265-dehydro-D-gluconate-builds acid from
2306115963ribitol-builds acid from
2306127613amygdalin-builds acid from
2306117057cellobiose-builds acid from
2306117108D-arabinose-builds acid from
2306118333D-arabitol-builds acid from
2306128847D-fucose-builds acid from
2306162318D-lyxose-builds acid from
230616731melezitose-builds acid from
2306128053melibiose-builds acid from
2306116634raffinose-builds acid from
2306132528turanose-builds acid from
2306165327D-xylose-builds acid from
2306116813galactitol-builds acid from
2306117113erythritol-builds acid from
2306128066gentiobiose-builds acid from
2306124265gluconate-builds acid from
2306117754glycerol-builds acid from
2306128087glycogen-builds acid from
2306115443inulin-builds acid from
2306130849L-arabinose-builds acid from
2306118403L-arabitol-builds acid from
2306118287L-fucose-builds acid from
2306117266L-sorbose-builds acid from
2306165328L-xylose-builds acid from
2306117716lactose-builds acid from
2306129864mannitol-builds acid from
2306143943methyl alpha-D-mannoside-builds acid from
2306126546rhamnose-builds acid from
2306130911sorbitol-builds acid from
2306117151xylitol-builds acid from
2306118305arbutin-builds gas from
2306115824D-fructose-builds gas from
2306117634D-glucose-builds gas from
2306116024D-mannose-builds gas from
2306116443D-tagatose-builds gas from
2306128260galactose-builds gas from
2306117268myo-inositol-builds gas from
2306117306maltose-builds gas from
23061320061methyl alpha-D-glucopyranoside-builds gas from
23061506227N-acetylglucosamine-builds gas from
2306133942ribose-builds gas from
2306117814salicin-builds gas from
2306128017starch-builds gas from
2306117992sucrose-builds gas from
2306127082trehalose-builds gas from
2306117632nitrate-reduction
2306118305arbutin+builds acid from
2306115824D-fructose+builds acid from
2306117634D-glucose+builds acid from
2306116024D-mannose+builds acid from
2306116443D-tagatose+builds acid from
2306128260galactose+builds acid from
2306117268myo-inositol+builds acid from
2306117306maltose+builds acid from
23061320061methyl alpha-D-glucopyranoside+builds acid from
23061506227N-acetylglucosamine+builds acid from
2306133942ribose+builds acid from
2306117814salicin+builds acid from
2306128017starch+builds acid from
2306117992sucrose+builds acid from
2306127082trehalose+builds acid from
23061casein+hydrolysis
230614853esculin+hydrolysis
230615291gelatin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12196216947citrate-carbon source
1219624853esculin-hydrolysis
121962606565hippurate-hydrolysis
12196217632nitrate-reduction
12196216301nitrite-reduction
12196217632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
2306135581indoleno
2306116136hydrogen sulfideno
2306115688acetoinno
12196235581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
2306115688acetoin-
12196215688acetoin-
12196217234glucose-

enzymes

@refvalueactivityec
23061catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
121962oxidase+
121962beta-galactosidase-3.2.1.23
121962alcohol dehydrogenase-1.1.1.1
121962gelatinase+/-
121962amylase-
121962DNase+
121962caseinase+3.4.21.50
121962catalase+1.11.1.6
121962tween esterase+
121962gamma-glutamyltransferase-2.3.2.2
121962lecithinase-
121962lipase+
121962lysine decarboxylase-4.1.1.18
121962ornithine decarboxylase-4.1.1.17
121962protease+
121962tryptophan deaminase-
121962urease+3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121962-+-+-------+---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121962-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121962------------------++------------+-----------------------+---+--------------+------+----------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4888water supplyColindaleUnited KingdomGBREurope
121962Environment, Water supplyUnited KingdomGBREurope1977

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_7607.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1861;97_4351;98_5569;99_7607&stattab=map
  • Last taxonomy: Virgibacillus proomii subclade
  • 16S sequence: AJ012667
  • Sequence Identity:
  • Total samples: 428
  • soil counts: 102
  • aquatic counts: 71
  • animal counts: 197
  • plant counts: 58

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
48881Risk group (German classification)
1219621Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Virgibacillus proomii genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 675AB367188675nuccore84407
20218Virgibacillus proomii genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 495AB367189495nuccore84407
20218Virgibacillus proomii isolate VP2 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceEU723673592nuccore84407
20218Virgibacillus proomii isolate VP3 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceEU723674439nuccore84407
20218Virgibacillus proomii isolate Vp26 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceEU723675884nuccore84407
23061Virgibacillus proomii 16S rRNA gene, strain LMG 12370AJ0126671506nuccore84407

GC content

  • @ref: 23061
  • GC-content: 37.0
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 4888

culture collection no.: DSM 13055, LMG 12370, CIP 106304

straininfo link

  • @ref: 71126
  • straininfo: 7106

literature

  • topic: Phylogeny
  • Pubmed-ID: 10425765
  • title: Proposal of Virgibacillus proomii sp. nov. and emended description of Virgibacillus pantothenticus (Proom and Knight 1950) Heyndrickx et al. 1998.
  • authors: Heyndrickx M, Lebbe L, Kersters K, Hoste B, De Wachter R, De Vos P, Forsyth G, Logan NA
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-49-3-1083
  • year: 1999
  • mesh: Animals, Bacillus/chemistry/*classification/cytology/physiology, Bacterial Proteins/analysis, Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Electrophoresis, Polyacrylamide Gel, Fatty Acids/analysis, Humans, Molecular Sequence Data, Phenotype, Phylogeny, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, Restriction Mapping
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4888Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13055)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13055
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
23061M. Heyndrickx,L. Lebbe,K. Kersters,B. Hoste,R. De Wachter,P. De Vos,G. Forsyth,N. A. Logan10.1099/00207713-49-3-1083Proposal of Virgibacillus proomii sp. nov. and emended description of Virgibacillus pantothenticus (Proom and Knight 1950) Heyndrickx et al. 1998IJSEM 49: 1083-1090 199910425765
39486Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18419
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
71126Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7106.1StrainInfo: A central database for resolving microbial strain identifiers
121962Curators of the CIPCollection of Institut Pasteur (CIP 106304)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106304